Chocolate’s secret ingredient is the fermenting microbes that make it taste so good

Home » Chocolate’s secret ingredient is the fermenting microbes that make it taste so good

Caitlin Clark, Colorado State University

Estimated reading time: 6 minutes

Whether baked as chips into a cookie, melted into a sweet warm drink or molded into the shape of a smiling bunny, chocolate is one of the world’s most universally consumed foods.

chocolate with milted chocolate on white ceramic plate
Photo by Pixabay on

Even the biggest chocolate lovers, though, might not recognize what this ancient food has in common with kimchi and kombucha: its flavors are due to fermentation. That familiar chocolate taste is thanks to tiny microorganisms that help transform chocolate’s raw ingredients into the much-beloved rich, complex final product.

In labs from Peru to Belgium to Ivory Coast, self-proclaimed chocolate scientists like me are working to understand just how fermentation changes chocolate’s flavor. Sometimes we create artificial fermentations in the lab. Other times we take cacao bean samples from real fermentations “in the wild.” Often, we make our experimental batches into chocolate and ask a few lucky volunteers to taste it and tell us what flavors they detect.

After decades of running tests like this, researchers have solved many of the mysteries that govern cacao fermentation, including which microorganisms participate and how this step governs chocolate flavor and quality.

From seed pod to chocolate bar

The food you know as chocolate starts its life as the seeds of football-shaped pods of fruit growing directly from the trunk of the Theobroma cacao tree. It looks like something Dr. Seuss would have designed. But as long as 3,900 years ago the Olmecs of Central America had figured out a multi-step process to transform these giant seed pods into an edible treat.

First, workers crack the brightly colored fruit open and scoop out the seeds and pulp. The seeds, now called “beans,” cure and drain over the course of three to 10 days before drying under the Sun. The dry beans are roasted, then crushed with sugar and sometimes dried milk until the mixture feels so smooth you can’t distinguish the particles on your tongue. At this point, the chocolate is ready to be fashioned into bars, chips or confections.

It’s during the curing stage that fermentation naturally occurs. Chocolate’s complex flavor consists of hundreds of individual compounds, many of which are generated during fermentation. Fermentation is the process of improving the qualities of a food through the controlled activity of microbes, and it allows the bitter, otherwise tasteless cacao seeds to develop the rich flavors associated with chocolate.

Microorganisms at work

Cacao fermentation is a multi-step process. Any compound microorganisms produced along the way that changes the taste of the beans will also change the taste of the final chocolate.

The first fermentation step may be familiar to home brewers, because it involves yeasts – some of them the same yeasts that ferment beer and wine. Just like the yeast in your favorite brew, yeast in a cacao fermentation produces alcohol by digesting the sugary pulp that clings to the beans.

This process generates fruity-tasting molecules called esters and floral-tasting fusel alcohols. These compounds soak into the beans and are later present in the finished chocolate.

As the pulp breaks down, oxygen enters the fermenting mass and the yeast population declines as oxygen-loving bacteria take over. These bacteria are known as acetic acid bacteria because they convert the alcohol generated by the yeast into acetic acid.

The acid soaks into the beans, causing biochemical changes. The sprouting plant dies. Fats agglomerate. Some enzymes break proteins down into smaller peptides, which become very “chocolatey”-smelling during the subsequent roasting stage. Other enzymes break apart the antioxidant polyphenol molecules, for which chocolate has gained renown as a superfood. As a result, contrary to its reputation, most chocolate contains very few polyphenols, or even none at all.

All the reactions kicked off by acetic acid bacteria have a major impact on flavor. These acids encourage the degradation of heavily astringent, deep purple polyphenol molecules into milder-tasting, brown-colored chemicals called o-quinones. Here is where cacao beans turn from bitter-tasting to rich and nutty. This flavor transformation is accompanied by a color shift from reddish-purple to brown, and it is the reason the chocolate you’re familiar with is brown and not purple.

Finally, as acid slowly evaporates and sugars are used up, other species – including filamentous fungi and spore-forming Bacillus bacteria – take over.

As vital as microbes are to the chocolate-making process, sometimes organisms can ruin a fermentation. An overgrowth of the spore-forming Bacillus bacteria is associated with compounds that lead to rancid, cheesy flavors.

Terroir of a place and its microbes

Cacao is a wild fermentation – farmers rely on natural microbes in the environment to create unique, local flavors. This phenomenon is known as “terroir”: the characteristic flair imparted by a place. In the same way that grapes take on regional terroir, these wild microbes, combined with each farmer’s particular process, confer terroir on beans fermented in each location.

Market demand for these fine, high-quality beans is growing. Makers of gourmet, small-batch chocolate hand-select beans based on their distinctive terroir in order to produce chocolate with an impressive range of flavor nuances.

If you’ve experienced chocolate only in the form of a bar you might grab near the grocery store checkout, you probably have little idea of the range and complexity that truly excellent chocolate can exhibit.

[Over 100,000 readers rely on The Conversation’s newsletter to understand the world. Sign up today.]

A bar from Akesson’s Madagascar estate may be reminiscent of raspberries and apricots, while Canadian chocolate-maker Qantu’s wild-fermented Peruvian bars taste like they’ve been soaked in Sauvignon Blanc. Yet in both cases, the bars contain nothing except cacao beans and some sugar.

This is the power of fermentation: to change, convert, transform. It takes the usual and make it unusual – thanks to the magic of microbes.The Conversation

Caitlin Clark, Ph.D. Candidate in Food Science, Colorado State University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Latest from Assorted Ideas, Large & Small

Balloon Girl, New York City, Fine art photography print/©Deborah Julian

Roosevelt Island Cherry Blossoms 2021

Cloudy weather ahead for NYC, but come enjoy a brief, sunny walk through the cherry blossoms

A sunny walk through the cherry blossoms is a public service. Because cloudy, even rainy weather this weekend dims the pleasures of Roosevelt Island’s peak, we shot this video for those who will miss it.

Keep reading
First Day of Spring, Central Park, New York City, 2021

Central Park, New York City, On the First Day of Spring, 2021

Yeah, crocuses poked out of the soil along Central Park’s pathways, but the first day of spring, 2021, blossomed with something else: People.

Keep reading
building with tree

The so-called experts strike again with a boost from the New York Times

In an op-ed in the New York Times, “Tasmanian Tiger Is Extinct. Why Do People Keep Seeing Them,” the so-called experts strike again. Scientists engage their inner know-it-all, and mass media helps them along.

Keep reading
purple and red balloons

Your Life’s A Popup. Don’t Worry. Grab Some Fun Now Because You Can Always Do It Again

Your life’s a popup, a one of a kind invention, a wrinkle in time. And what’s great is you can screw up, win, lose or draw and, then, do it again.

Keep reading

What is the source of wisdom? And let it flow free…

The source of wisdom? What is it? I’ve wondered about it since messages first came to me, clear and easy, out of the blue, years ago. Like art, I know it when I see it, but I still don’t know what it really is. Or where it comes…

Keep reading


Something went wrong. Please refresh the page and/or try again.

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.